Thermo Fisher Scientific's new mass spectrometer the LTQ XL with electron transfer dissociation (ETD), won silver at the Pittcon Editors' Awards because it promises to provide a breakthrough in proteomics research. The technology will dramatically increase the sequence coverage for proteins while providing more specific information about the nature and site of post-translational protein modifications.

Post-translational modifications, such as glycosylation and phosphorylation, are reversible protein modifications that are used in cell signalling pathways. Because the modifications are reversible positional information of where these modifications occur is often lost in MS fragmentation peptide sequencing studies.

The instrument combines ETD techniques with collisionally induced dissociation (CID) and Pulsed-Q Dissociation (PQD) on a linear ion trap mass spectrometer. The instrument also takes advantage of the high ion storage capacity and fast cycle times of the linear ion trap allowing researchers to conduct rapid, alternating fragmentation experiments during liquid chromatography (LC)/MS.

"We believe ETD performed on a linear ion trap is a major turning point for the proteomics community, enabling researchers to pinpoint, identify and fully characterise more post-transitional modificatons such as phosphorylation and glycosylation than ever before," said Greg Herrema, president of Scientific Instruments at Thermo Fisher Scientific.

The ETD technique works by introducing negatively charged fluoranthene anions into the LTQ linear ion trap along with positive, multiply charged peptide cations. An electron from the fluoranthene is transferred to the peptide cation before the 'gentle' dissociation causes the peptide to fragment while preserving the integrity of post-translational modifications on the peptide fragment.

The ion trap allows precise control of these reactions improving the efficiency of the ETD reactions. Positively charged peptide cations are injected and isolated at the centre of the trap before being transferred into the front section of the trap.

A quadrupole mass filter purifies the fluoranthene reagent anions from the chemical ionisation (CI) source before they are injected and isolated at the centre section. The peptide cations are then moved back into the centre section where the ion-ion reactions occur.

A recent study published in 'Cell' on 3 November 2006 by Matthias Mann and coworkers, of the Max Planck Institute for Biochemistry, showed that 6,600 phosphorylation sites could be identified on 2,284 proteins using the technique.

The approach allowed the identification of key phosphorylation events in signalling pathways and is general enough to be able to be applied to any cell culture system that can be SILAC (stable isotope labelling with amino acids in cell culture) labelled.

The new system takes advantage of the large ion storage capacity and fast cycle times of the triply segmented linear ion trap to allow the rapid alternation between collisionally induced dissociation (CID) and ETD scanning throughout the LC/MS analysis of complex biological samples.

The mass spectra obtained from each technique are complementary, with the b and y fragment ion spectra from the CID experiment complimenting the c and z fragment ion spectra from ETD. This increases the coverage for each protein by giving a more comprehensive analysis of each sample.

The technique can also be used to study cross talking between signals, perturbations caused by drug binding, genetic knockouts or small interfering RNA (siRNA) knockdowns of signalling molecules.

"Within five years everyone will be using ETD for proteomics research," predicts Dr Ian Jardine, vice president of Global R&D at Thermo Fisher Scientific.